Genetic Variant ENSG00000253968:n.446+1804T>A (chr5-173508176-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000827042.1(ENSG00000253968):n.446+1804T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,912 control chromosomes in the GnomAD database, including 10,385 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 10385 hom., cov: 31)

Consequence

ENSG00000253968
ENST00000827042.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.13

Variant links:

Genes affected

ENSG00000253968 (HGNC:):

ENSG00000253968 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377732	XR_001743001.1 link	n.3056+586T>A		intron_variant	Intron 14 of 14
LOC105377732	XR_007059057.1 link	n.4116+586T>A		intron_variant	Intron 17 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253968	ENST00000827042.1 link	n.446+1804T>A		intron_variant	Intron 2 of 2
ENSG00000253968	ENST00000827044.1 link	n.374+1804T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.365

AC:

55468

AN:

151794

Hom.:

10362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.462

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.272

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.388

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.389

Gnomad OTH

AF:

0.387

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.366

AC:

55538

AN:

151912

Hom.:

10385

Cov.:

AF XY:

0.369

AC XY:

27381

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.293

AC:

12165

AN:

41448

American (AMR)

AF:

0.462

AC:

7056

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

1139

AN:

3466

East Asian (EAS)

AF:

0.272

AC:

1404

AN:

5170

South Asian (SAS)

AF:

0.403

AC:

1944

AN:

4818

European-Finnish (FIN)

AF:

0.388

AC:

4084

AN:

10514

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.389

AC:

26434

AN:

67912

Other (OTH)

AF:

0.392

AC:

827

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1766

3532

5299

7065

8831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.384

Hom.:

1401

Bravo

AF:

0.368

Asia WGS

AF:

0.346

AC:

1204

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.0

(source)

DANN

Benign

0.65

PhyloP100

1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chr5-173508176-T-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

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